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Nickel in PDB 3ze6: 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms

Enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms

All present enzymatic activity of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms:
1.12.7.2;

Protein crystallography data

The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms, PDB code: 3ze6 was solved by M.C.Marques, R.Coelho, I.A.C.Pereira, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.51 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.170, 97.350, 102.970, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 15.4

Other elements in 3ze6:

The structure of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms also contains other interesting chemical elements:

Iron (Fe) 18 atoms
Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms (pdb code 3ze6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms, PDB code: 3ze6:

Nickel binding site 1 out of 1 in 3ze6

Go back to Nickel Binding Sites List in 3ze6
Nickel binding site 1 out of 1 in the 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 3D Structure of the Ni-Fe-Se Hydrogenase From D. Vulgaris Hildenborough in the As-Isolated Oxidized State at 1.50 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:9.4
occ:1.00
 SD B:PSW489 2.1 7.7 0.2
SD B:PSW489 2.1 8.1 0.7
SG B:CYS492 2.2 7.1 1.0
SG B:OCS75 2.2 8.7 1.0
SG B:CYS78 2.3 7.2 1.0
SE B:PSW489 2.4 9.4 0.7
FE B:FCO500 2.4 7.8 1.0
SE B:PSW489 2.4 15.8 0.1
HB1C B:PSW489 3.0 8.9 0.2
HB2 B:OCS75 3.1 9.4 1.0
HB2C B:PSW489 3.1 8.9 0.2
OD1 B:OCS75 3.1 10.7 1.0
OD3 B:OCS75 3.1 9.5 1.0
CB B:OCS75 3.2 7.8 1.0
C1 B:FCO500 3.2 8.2 1.0
CB B:PSW489 3.3 7.4 0.2
HB2 B:CYS492 3.3 7.5 1.0
SE B:PSW489 3.3 20.0 0.2
HB3 B:CYS78 3.3 7.8 1.0
C2 B:FCO500 3.4 6.8 1.0
CB B:CYS492 3.4 6.2 1.0
HB3 B:OCS75 3.4 9.4 1.0
HB2C B:PSW489 3.5 8.1 0.7
CB B:CYS78 3.5 6.5 1.0
H B:CYS78 3.5 8.7 1.0
CB B:PSW489 3.6 6.7 0.7
HB1C B:PSW489 3.7 11.2 0.1
H B:CYS492 3.8 6.7 1.0
CB B:PSW489 3.8 9.4 0.1
HD2 B:ARG422 3.9 8.9 1.0
HB1C B:PSW489 4.0 8.1 0.7
HB B:VAL77 4.1 8.0 1.0
N1 B:FCO500 4.1 9.0 1.0
HB3 B:CYS492 4.1 7.5 1.0
N B:CYS78 4.1 7.3 1.0
C3 B:FCO500 4.1 7.6 1.0
HE2 B:HIS82 4.2 9.5 1.0
HB2 B:CYS78 4.2 7.8 1.0
N2 B:FCO500 4.3 7.0 1.0
HB2C B:PSW489 4.4 11.2 0.1
N B:CYS492 4.4 5.5 1.0
CA B:CYS78 4.4 7.2 1.0
CA B:CYS492 4.4 6.3 1.0
HA B:CYS492 4.6 7.5 1.0
CA B:OCS75 4.6 6.9 1.0
HH11 B:ARG422 4.6 9.1 1.0
CD B:ARG422 4.7 7.4 1.0
H B:VAL77 4.8 8.4 1.0
CA B:PSW489 4.8 7.8 0.2
HD3 B:ARG422 4.8 8.9 1.0
O B:PSW489 4.8 7.7 1.0
HD2 B:HIS82 4.9 7.7 1.0
CA B:PSW489 4.9 7.8 0.7
NE2 B:HIS82 4.9 7.9 1.0
CA B:PSW489 4.9 7.8 0.1
HA B:OCS75 4.9 8.3 1.0
CB B:VAL77 5.0 6.7 1.0

Reference:

M.C.Marques, R.Coelho, I.A.C.Pereira, P.M.Matias. Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough Int.J.Hydrogen Energy 2013.
ISSN: ISSN 0360-3199
DOI: 10.1016/J.IJHYDENE.2013.04.132
Page generated: Wed Oct 9 17:54:56 2024

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